Extensin_2 - PFAM28P - GREMLIN Contacts

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Extensin_2 - Extensin-like region

PFAM:	PF04554	Sequences: YVYKSPPPPYYSSPSPKYVYKSPPPPTPYVYKSPPPPYYVYKSPPPPPPYVYKSPPPP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	58 (53)
Sequences:	622 (196)
Seq/√Len:	27.0
META:	0.051

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_V	51_V	3.315	1.00
18_Y	50_Y	2.229	0.98
30_V	51_V	2.010	0.96
22_S	33_S	1.897	0.95
2_V	30_V	1.846	0.94
2_V	19_V	1.818	0.93
22_S	43_S	1.720	0.91
33_S	43_S	1.646	0.89
29_Y	33_S	1.611	0.88
18_Y	21_K	1.575	0.87
22_S	25_P	1.563	0.86
5_S	8_P	1.435	0.81
19_V	30_V	1.408	0.80
21_K	53_K	1.405	0.80
43_S	46_P	1.371	0.78
11_Y	15_S	1.365	0.78
33_S	54_S	1.359	0.77
10_Y	13_S	1.310	0.75
47_P	50_Y	1.232	0.70
32_K	53_K	1.215	0.69
54_S	58_P	1.204	0.68
55_P	58_P	1.116	0.62
32_K	38_Y	1.082	0.60
4_K	21_K	1.063	0.58
52_Y	58_P	1.029	0.56
1_Y	5_S	1.017	0.55
37_P	53_K	1.014	0.55
45_P	50_Y	1.013	0.55
25_P	31_Y	1.003	0.54
21_K	42_K	0.956	0.50
22_S	54_S	0.947	0.50
10_Y	38_Y	0.929	0.48
52_Y	55_P	0.912	0.47
32_K	39_Y	0.907	0.47
20_Y	31_Y	0.886	0.45
4_K	9_P	0.883	0.45
43_S	54_S	0.872	0.44
13_S	18_Y	0.866	0.44
39_Y	53_K	0.856	0.43
5_S	22_S	0.852	0.42
15_S	34_P	0.847	0.42
5_S	9_P	0.844	0.42
2_V	51_V	0.844	0.42
38_Y	45_P	0.840	0.42
31_Y	37_P	0.838	0.41
5_S	35_P	0.826	0.41
3_Y	20_Y	0.820	0.40
22_S	28_P	0.815	0.40
47_P	53_K	0.807	0.39
24_P	35_P	0.803	0.39
22_S	31_Y	0.799	0.39
16_P	20_Y	0.774	0.37
26_P	57_P	0.769	0.37
1_Y	4_K	0.748	0.35
39_Y	42_K	0.740	0.35
9_P	26_P	0.724	0.33
7_P	16_P	0.712	0.33
11_Y	39_Y	0.703	0.32
14_P	37_P	0.696	0.32
1_Y	8_P	0.677	0.30
15_S	18_Y	0.677	0.30
38_Y	42_K	0.665	0.30
26_P	37_P	0.660	0.29
46_P	51_V	0.634	0.28
29_Y	50_Y	0.634	0.28
3_Y	13_S	0.615	0.27
37_P	52_Y	0.612	0.26
42_K	45_P	0.611	0.26
12_S	17_K	0.607	0.26
21_K	29_Y	0.605	0.26
36_P	55_P	0.574	0.24
4_K	42_K	0.567	0.24
17_K	28_P	0.543	0.23
4_K	12_S	0.534	0.22
16_P	36_P	0.531	0.22
24_P	56_P	0.525	0.22
18_Y	36_P	0.520	0.21
20_Y	42_K	0.517	0.21
35_P	50_Y	0.507	0.21
2_V	17_K	0.500	0.20

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2bn5B	1	0.2759	0.6	0.895	Contact Map
1twfA	1	0	0.5	0.904	Contact Map
1ozjA	1	0.1379	0.4	0.906	Contact Map
1rxtA	1	0.3448	0.3	0.916	Contact Map
4hd4A	1	0.1207	0.3	0.921	Contact Map
3iu1A	1	0.3448	0.3	0.921	Contact Map
4c68A	1	0.3448	0.3	0.921	Contact Map
4c7iA	1	0.3448	0.3	0.921	Contact Map
4irgA	2	0.2586	0.2	0.926	Contact Map
4irhA	2	0.2759	0.2	0.926	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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